{ "abstract": "African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. Asian rice (Oryza sativa), which was introduced in Africa when European settlers arrived, gradually replaced African rice and has since dominated rice cultivation in the continent. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we show that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 87 AfXoo genomes identified five main populations, including highly clonal ones, and a more diverse and recombinant population. Tip-dating analysis revealed that the AfXoo population went through a period of expansion, then decline and more recent recovery. We hypothesize this followed the rise and fall of African rice, and that the introduction of O. sativa served as a bottleneck leading to the emergence of current AfXoo populations. We show that AfXoo has a highly conserved repertoire of type III effectors (T3E), but that nonetheless there is variation especially between populations. In the case of transcription activator-like effectors (TALEs), variation can arise quickly through rearrangements, and we hypothesize that the TALE repertoire of AfXoo has been selected to allow the bacteria to colonize both species of cultivated rice found in the continent. Our research provides an attempt to decipher the genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region. Author summary: For thousands of years, rice cultivation has been an integral part of African agriculture. However, the cultivation of the locally domesticated African rice cultivar (Oryza glaberrima) has gradually shifted towards Asian rice varieties (Oryza sativa), likely altering associated microbe populations. One of these microbes is the causal agent of bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo). We performed a population genomics analysis to understand the evolutionary history of African strains of Xoo (AfXoo). We show that current populations of AfXoo have relatively low genetic diversity, have distinct virulence genes, and have historically gone through expansion and decline. We propose AfXoo was first adapted to African rice at least a thousand years ago. The introduction of O. sativa then shaped the recent population dynamics of AfXoo. Our results highlight the interplay between crop domestication and cultivation and pathogen evolution.", "abstract_shown": true, "affiliations": [ "Plant Health Institute of Montpellier, University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France", "Laboratoire de Biologie Moléculaire Appliquée, Faculté des Sciences et Techniques, Université des Sciences et Techniques et des technologies de Bamako, Bamako, Mali", "Institut Supérieur Agronomique et Vétérinaire « Valéry Giscard d’Estaing » de Faranah (ISAV « VGE »/F), Faranah, République de Guinée", "Pathogens Genomic Diversity Network Africa, Bamako, Mali", "Université de Tilaberi, Tillabéri, Niger", "Laboratoire de Biologie Moléculaire Appliquée, Faculté de Médecine et d'Odontostomatologie, Université des Sciences et Techniques et des Technologies de Bamako, Bamako, Mali", "Institut Sénégalais de Recherches Agricoles, Tambacounda, Senegal", "Centre National de Recherche Scientifique et Technologique (CNRST)/ Institut de l’Environnement et de Recherches Agricoles (INERA), Bobo Dioulasso, Burkina Faso", "Laboratoire de Biologie Moléculaire Appliquée et Centre de Recherche en Santé Globale, Bamako, Mali", "Laboratoire de Physiologie Végétale, Université Félix Houphouët-Boigny, Abidjan, Côte d'Ivoire", "Centre Régional de Recherche Agricole de Niono, Institut d'Economie Rurale, Bamako, Mali" ], "article_type": "Research Article", "arxiv": null, "author_total": 23, "authors": [ { "affs": [ 0 ], "name": "Ian Lorenzo Quibod" }, { "affs": [ 1 ], "name": "Coline Sciallano" }, { "affs": [ 2 ], "name": "Florence Auguy" }, { "affs": [ 3 ], "name": "Laurent Brottier" }, { "affs": [ 4 ], "name": "Alexis Dereeper" }, { "affs": [ 5 ], "name": "Diariatou Diagne" }, { "affs": [ 6 ], "name": "Amadou Diallo" }, { "affs": [ 7 ], "name": "Hinda Doucouré" }, { "affs": [ 8 ], "name": "Solely Issaka Mayaki" }, { "affs": [ 9 ], "name": "Ibrahim Keita" }, { "affs": [ 10 ], "name": "Lazeni Konate" }, { "name": "Hamidou Tall" }, { "name": "Cheick Tékété" }, { "name": "Sylvain Zougrana" }, { "name": "Mathilde Hutin" }, { "name": "Ousmane Koita" }, { "name": "Daoudou Kone" }, { "name": "Soungalo Sarra" }, { "name": "Valérie Verdier" }, { "name": "Issa Wonni" }, { "name": "Boris Szurek" }, { "name": "Sébastien Cunnac" }, { "name": "Alvaro L. Pérez-Quintero" } ], "bibtex": "https://research.draconitic.com/paper/1jc324v4vrcmx.bib", "cited_by": 0, "doi": "10.1371/journal.ppat.1014015", "fulltext_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014015", "id": "1jc324v4vrcmx", "issns": [ "1553-7374" ], "landing_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014015", "language": null, "licence": "CC-BY-4.0", "licence_label": "CC BY 4.0", "licence_source": "journal", "licence_url": "https://creativecommons.org/licenses/by/4.0/", "metadata_licence": null, "native_subjects": [ [ "openalex", "1110|Plant Pathogenic Bacteria Studies" ], [ "plos", "/Biology and life sciences/Biochemistry/Nucleic acids/DNA/DNA recombination" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Evolutionary systematics/Phylogenetics" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Biology and life sciences/Evolutionary biology/Population genetics" ], [ "plos", "/Biology and life sciences/Genetics/DNA/DNA recombination" ], [ "plos", "/Biology and life sciences/Genetics/Genomics" ], [ "plos", "/Biology and life sciences/Genetics/Population genetics" ], [ "plos", "/Biology and life sciences/Organisms/Bacteria/Xanthomonas" ], [ "plos", "/Biology and life sciences/Organisms/Eukaryota/Plants/Grasses/Rice" ], [ "plos", "/Biology and life sciences/Population biology/Population genetics" ], [ "plos", "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics" ], [ "plos", "/Biology and life sciences/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics" ], [ "plos", "/Computer and information sciences/Data management/Taxonomy/Evolutionary systematics/Phylogenetics/Phylogenetic analysis" ], [ "plos", "/People and places/Geographical locations/Africa" ], [ "plos", "/Research and analysis methods/Animal studies/Experimental organism systems/Plant and algal models/Rice" ] ], "openalex": "W7213447867", "pdf_url": "https://journals.plos.org/plospathogens/article/file?id=10.1371/journal.ppat.1014015&type=printable", "pmcid": null, "pmid": null, "published": "2026-09-17", "publisher": "Public Library of Science", "ris": "https://research.draconitic.com/paper/1jc324v4vrcmx.ris", "sources": [ { "first_seen": "2026-10-30T12:17:49Z", "native_id": "10.1371/journal.ppat.1014015", "source": "plos", "url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1014015" } ], "subjects": [ { "field": "biology", "origin": "plos:evolutionary biology", "subfield": "evolutionary-biology" }, { "field": "biology", "origin": "plos:genetics", "subfield": "genetics-genomics" } ], "title": "Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa", "title_text": "Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa", "type": "peer-reviewed", "updated_at": "2026-10-30T12:17:49Z", "url": "https://research.draconitic.com/paper/1jc324v4vrcmx", "venue": "PLOS Pathogens", "versions": [] }